4X0A

Structure of tRNA-processing enzyme complex 6

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 

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This is version 1.2 of the entry. See complete history. 


Literature

Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.

Yamashita, S., Martinez, A., Tomita, K.

(2015) Structure 23: 830-842

  • DOI: https://doi.org/10.1016/j.str.2015.03.013
  • Primary Citation of Related Structures:  
    4WBY, 4WBZ, 4WC0, 4WC1, 4WC2, 4WC3, 4WC4, 4WC5, 4WC6, 4WC7, 4X0A, 4X0B

  • PubMed Abstract: 

    • The 3'-terminal CCA (C74C75A76-3') of tRNA is required for protein synthesis. In Aquifex aeolicus, the CCA-3' is synthesized by CC-adding and A-adding enzymes, although in most organisms, CCA is synthesized by a single CCA-adding enzyme. The mechanisms by which the A-adding enzyme adds only A76, but not C74C75, onto tRNA remained elusive ...

    The 3'-terminal CCA (C74C75A76-3') of tRNA is required for protein synthesis. In Aquifex aeolicus, the CCA-3' is synthesized by CC-adding and A-adding enzymes, although in most organisms, CCA is synthesized by a single CCA-adding enzyme. The mechanisms by which the A-adding enzyme adds only A76, but not C74C75, onto tRNA remained elusive. The complex structures of the enzyme with various tRNAs revealed the presence of a single tRNA binding site on the enzyme, with the enzyme measuring the acceptor-TΨC helix length of tRNA. The 3'-C75 of tRNA lacking A76 can reach the active site and the size and shape of the nucleotide binding pocket at the insertion stage are suitable for ATP. The 3'-C74 of tRNA lacking C75A76 cannot reach the active site, although CTP or ATP can bind the active pocket. Thus, the A-adding enzyme adds only A76, but not C74C75, onto tRNA.

    Organizational Affiliation: 

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan. Electronic address: kozo-tomita@aist.go.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly A polymerase396Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: pcnB1, aq_411
EC: 2.7.7
UniProt
Find proteins for O66728 (Aquifex aeolicus (strain VF5))
Explore O66728 
Go to UniProtKB:  O66728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66728
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (73-MER)73Thermotoga maritima MSB8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.05α = 90
b = 110.3β = 90
c = 123.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Database references
  • Version 1.2: 2019-11-20
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy